Substantially less bins found with v2.1.0 vs v2.0.2

[paulzierep]

We are using semibin in our MAGs workflow: https://iwc.galaxyproject.org/workflow/mags-building-main/
And found that there is a large difference between v2.1.0 vs v2.0.2 for bin creation in terms of numbers as well as quality.
Here is an example of a real-life analysis of the bee microbiome using checkm2.
Any idea why this could be the case?

v2.1.0

Name	Completeness	Contamination	Completeness_Model_Used	Translation_Table_Used	Coding_Density	Contig_N50	Average_Gene_Length	Genome_Size	GC_Content	Total_Coding_Sequences	Total_Contigs	Max_Contig_Length	Additional_Notes
SemiBin_0	29.34	3.36	Neural Network (Specific Model)	11	0.865	3922	274.72700296735906	641692	0.42	674	154	23611	None
SemiBin_1	50.36	19.25	Neural Network (Specific Model)	11	0.831	4102	268.05308588692276	2238014	0.45	2317	530	26601	None
SemiBin_1024	16.65	4.62	Neural Network (Specific Model)	11	0.761	4297	219.95294117647057	1030336	0.3	1190	235	22552	None
SemiBin_1025	46.0	8.8	Neural Network (Specific Model)	11	0.881	4617	251.60856720827178	1157997	0.36	1354	262	16146	None
SemiBin_1026	53.4	10.87	Neural Network (Specific Model)	11	0.904	8172	302.56342412451363	1289043	0.37	1285	201	51180	None
SemiBin_2	10.53	0.07	Neural Network (Specific Model)	11	0.787	6811	225.45338208409507	468390	0.36	547	84	36178	None
SemiBin_4090	79.38	32.26	Neural Network (Specific Model)	11	0.868	11804	297.6619880349747	4464082	0.35	4346	544	130205	None
SemiBin_4091	33.39	0.62	Neural Network (Specific Model)	11	0.88	6398	275.74976744186046	1009154	0.38	1075	180	33958	None
SemiBin_4327	3.93	0.0	Neural Network (Specific Model)	11	0.776	239878	320.9846153846154	239878	0.52	195	1	239878	None
SemiBin_5113	20.99	0.71	Neural Network (Specific Model)	11	0.837	6513	275.096018735363	840777	0.41	854	138	80687	None
SemiBin_5114	45.57	0.55	Neural Network (Specific Model)	11	0.893	28063	278.17007874015746	592880	0.45	635	37	61370	None
SemiBin_6133	46.26	0.0	Neural Network (Specific Model)	11	0.885	11768	296.1252093802345	2395077	0.6	2388	266	33128	None
SemiBin_6135	31.31	3.13	Neural Network (Specific Model)	11	0.877	5849	269.575104727708	1537517	0.42	1671	263	113188	None
SemiBin_6136	37.3	0.0	Neural Network (Specific Model)	11	0.907	4375	280.7223032069971	1270666	0.42	1372	296	13692	None
SemiBin_6137	17.79	1.83	Neural Network (Specific Model)	11	0.863	4201	273.00318133616116	892578	0.56	943	217	16432	None
SemiBin_6138	32.29	1.2	Neural Network (Specific Model)	11	0.881	38873	292.14128595600675	2345787	0.54	2364	124	124190	None

v2.0.2

Name	Completeness	Contamination	Completeness_Model_Used	Translation_Table_Used	Coding_Density	Contig_N50	Average_Gene_Length	Genome_Size	GC_Content	Total_Coding_Sequences	Total_Contigs	Max_Contig_Length	Additional_Notes
SemiBin_0	23.79	0.12	Neural Network (Specific Model)	11	0.817	3258	251.88888888888889	398745	0.4	432	117	6680	None
SemiBin_1	52.09	5.87	Neural Network (Specific Model)	11	0.834	6426	283.44331133773244	1696173	0.46	1667	281	30922	None
SemiBin_11	67.74	0.33	Gradient Boost (General Model)	11	0.91	4546	280.95963933018464	2152417	0.42	2329	489	13692	None
SemiBin_12	65.58	3.54	Neural Network (Specific Model)	11	0.873	5107	280.06475300400535	1439659	0.43	1498	297	17316	None
SemiBin_13	87.69	5.74	Neural Network (Specific Model)	11	0.864	46666	304.42977420589364	2757890	0.34	2613	86	195230	None
SemiBin_15	12.79	2.58	Neural Network (Specific Model)	11	0.711	3512	224.34619883040935	808039	0.42	855	223	13385	None
SemiBin_16	10.88	0.44	Neural Network (Specific Model)	11	0.768	4943	239.263862332696	487844	0.29	523	102	19894	None
SemiBin_19	12.3	1.7	Neural Network (Specific Model)	11	0.857	22925	261.6875687568757	830477	0.5	909	56	74194	None
SemiBin_2	20.56	0.1	Neural Network (Specific Model)	11	0.807	6054	260.4830028328612	681860	0.39	706	119	32058	None
SemiBin_20	13.6	0.85	Neural Network (Specific Model)	11	0.836	3764	263.53846153846155	1005195	0.56	1066	253	33621	None
SemiBin_21	100.0	0.4	Neural Network (Specific Model)	11	0.888	52033	316.9252607184241	5536488	0.56	5178	167	176966	None
SemiBin_22	53.62	3.99	Neural Network (Specific Model)	11	0.849	4708	269.8386225523295	1409261	0.42	1481	307	23489	None
SemiBin_23	37.38	0.0	Neural Network (Specific Model)	11	0.88	3904	262.1492042440318	1344765	0.43	1508	341	10874	None
SemiBin_233	6.91	0.08	Neural Network (Specific Model)	11	0.761	239878	306.86	479658	0.51	400	4	239878	None
SemiBin_24	81.74	1.94	Neural Network (Specific Model)	11	0.887	6522	275.62341078474356	2124102	0.38	2281	367	33958	None
SemiBin_29	96.74	1.68	Neural Network (Specific Model)	11	0.881	12196	293.2869528441531	4714596	0.6	4729	491	79088	None
SemiBin_3	80.58	7.3	Neural Network (Specific Model)	11	0.903	7158	293.48175725986596	1307590	0.37	1343	214	24699	None
SemiBin_30	28.56	0.04	Neural Network (Specific Model)	11	0.832	4046	260.3989417989418	885576	0.46	945	220	11911	None
SemiBin_31	86.54	3.07	Neural Network (Specific Model)	11	0.901	17391	292.4266284896206	1358660	0.34	1397	127	64643	None
SemiBin_32	22.89	0.05	Neural Network (Specific Model)	11	0.824	5774	279.81328320802004	811680	0.41	798	148	30462	None
SemiBin_33	7.85	0.0	Neural Network (Specific Model)	11	0.75	4030	247.1933962264151	209245	0.3	212	55	5922	None
SemiBin_36	23.99	0.23	Neural Network (Specific Model)	11	0.913	5113	297.3452380952381	491923	0.37	504	99	31381	None
SemiBin_37	5.63	0.02	Neural Network (Specific Model)	11	0.863	113197	290.98623853211006	220395	0.35	218	13	113197	None
SemiBin_39	61.87	3.91	Neural Network (Specific Model)	11	0.912	4470	276.1839622641509	961775	0.37	1060	213	22627	None
SemiBin_4	29.73	0.11	Neural Network (Specific Model)	11	0.902	3547	256.61322081575247	605910	0.37	711	162	10396	None
SemiBin_42	22.28	1.33	Neural Network (Specific Model)	11	0.91	4408	296.7756183745583	553209	0.36	566	126	12478	None
SemiBin_44	100.0	0.79	Neural Network (Specific Model)	11	0.861	53399	318.0313479623824	3529330	0.39	3190	110	187436	None
SemiBin_45	36.59	4.63	Neural Network (Specific Model)	11	0.883	3979	289.0352526439483	833778	0.6	851	202	28432	None
SemiBin_5	72.88	29.28	Neural Network (Specific Model)	11	0.84	4332	278.1305147058824	2696139	0.46	2720	614	26601	None
SemiBin_50	6.25	0.0	Neural Network (Specific Model)	11	0.835	4959	274.4099099099099	218478	0.44	222	49	14929	None
SemiBin_51	6.58	0.14	Neural Network (Specific Model)	11	0.865	19562	244.65814696485623	264835	0.4	313	24	34399	None
SemiBin_52	4.58	0.02	Neural Network (Specific Model)	11	0.686	4255	221.66666666666666	264129	0.39	273	65	9536	None
SemiBin_53	9.26	0.12	Neural Network (Specific Model)	11	0.744	5827	241.62303664921467	371780	0.28	382	71	18159	None
SemiBin_54	14.45	0.13	Neural Network (Specific Model)	11	0.91	4727	316.46264367816093	362811	0.36	348	77	16911	None
SemiBin_55	49.85	0.59	Neural Network (Specific Model)	11	0.875	5967	275.24599708879185	1294529	0.35	1374	241	22855	None
SemiBin_56	94.46	15.69	Neural Network (Specific Model)	11	0.867	38965	320.2335025380711	2835660	0.34	2561	149	168383	None
SemiBin_57	10.63	0.35	Neural Network (Specific Model)	11	0.862	6291	270.52452025586354	441008	0.52	469	74	19904	None
SemiBin_6	47.36	13.44	Neural Network (Specific Model)	11	0.861	5540	270.496338028169	1671343	0.33	1775	315	57389	None
SemiBin_60	7.23	0.08	Neural Network (Specific Model)	11	0.898	8503	249.22	332324	0.39	400	51	35261	None
SemiBin_69	62.21	3.3	Neural Network (Specific Model)	11	0.888	5392	260.7740885416667	1350459	0.36	1536	265	19350	None
SemiBin_7	87.95	2.29	Neural Network (Specific Model)	11	0.897	25417	287.10086004691163	1225954	0.46	1279	84	80957	None
SemiBin_70	7.88	0.02	Neural Network (Specific Model)	11	0.861	7058	259.63141993957703	298880	0.36	331	46	41450	None
SemiBin_71	11.3	0.35	Neural Network (Specific Model)	11	0.877	11107	259.26720647773277	655290	0.52	741	77	34926	None
SemiBin_77	9.55	0.21	Neural Network (Specific Model)	11	0.881	10779	317.185303514377	337566	0.36	313	35	147518	None
SemiBin_9	33.38	9.66	Neural Network (Specific Model)	11	0.862	6382	280.41838134430725	1421971	0.33	1458	247	33203	None
SemiBin_91	5.58	0.03	Neural Network (Specific Model)	11	0.806	3565	245.2053872053872	270421	0.32	297	75	8490	None